AMBER Archive (2004)

Subject: Re: AMBER: methane box

From: FyD (
Date: Wed May 05 2004 - 10:36:08 CDT


> I want to create a hydrophobic solvent box, especiaaly methane to
> mimick
> the hydrophobic environment of peptides. How we can create a periodic
> solvent box of methane molecules? Is there any existing library for
> the same in amber6 or amber7?

I would say:
- optimize Methane to the 6-31G* theory level and get the RESP charges
- load the Tripos (with charges and atom types in it) format of CH4 in leap (if
you have have amber8) or the PDB file of CH4 (you have to add the atom types and
charges after loading the PDB file in this case) if you have amber5-7.
- solvate the structure 'by itself' (SolvateBox Methane Methane 10) and save the
prmtop and prmcrd files.
- run a 'cst volume' MD run from 100 to 300K to equilibrate
- run a 'cst pressure' MD run at 300 K to equilibrate to get the correct

It should be OK, Regards, Francois

F.-Y. Dupradeau
The Scripps Research Institute, San Diego, CA
Faculte de Pharmacie, UPJV, Amiens, France
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